new_ode_model: Create new ODE model

Description

Create new ODE model

Usage

new_ode_model(
  model = NULL,
  code = NULL,
  pk_code = NULL,
  dose_code = NULL,
  file = NULL,
  func = NULL,
  state_init = NULL,
  parameters = NULL,
  reparametrization = NULL,
  mixture = NULL,
  units = NULL,
  size = NULL,
  lagtime = NULL,
  obs = list(cmt = 1, scale = 1),
  dose = list(cmt = 1),
  covariates = NULL,
  declare_variables = NULL,
  iiv = NULL,
  iov = NULL,
  development = NULL,
  omega_matrix = NULL,
  ruv = NULL,
  ltbs = NULL,
  misc = NULL,
  cmt_mapping = NULL,
  int_step_size = NULL,
  default_parameters = NULL,
  fixed = NULL,
  cpp_show_code = FALSE,
  package = NULL,
  test_file = NULL,
  install = TRUE,
  folder = NULL,
  lib_location = NULL,
  verbose = FALSE,
  as_is = FALSE,
  nonmem = NULL,
  comments = NULL,
  version = "0.1.0",
  quiet = "",
  definition = NULL
)

Value

If package name is NULL, returns the model object. Otherwise has no return value.

Arguments

model: model name from model library
code: C++ code specifying ODE system
pk_code: C++ code called at any event
dose_code: C++ code called at dose event only
file: file containing C++ code
func: R function to be used with deSolve library
state_init: vector of state init
parameters: list or vector of parameter values
reparametrization: list of parameters with definitions that reparametrize the linear PK model to a 1-, 2- o4 3-compartment PK with standardized parametrization.
mixture: for mixture models, provide a list of the parameter associated with the mixture and it's possible values and probabilities (of the first value), e.g. list(CL = list(value = c(10, 20), probability = 0.3).
units: list or vector of parameter units
size: size of state vector for model. Size will be extracted automatically from supplied code, use this argument to override.
lagtime: lag time
obs: list with "scale": character string with definition for scale, e.g. "V" or "V*(WT/70)". If NULL, scale defaults to 1., and "cmt" the observation compartment
dose: specify default dose compartment, e.g. list(cmt = 1)
covariates: specify covariates, either as a character vector or a list. if specified as list, it allows use of timevarying covariates (see new_covariate() function for more info)
declare_variables: declare variables
iiv: inter-individual variability, can optionally be added to library
iov: inter-occasion variability, can optionally be added to library
development: Information about the model development population, can optionally be added to library
omega_matrix: variance-covariance matrix for inter-individual variability, can optionally be added to library
ruv: residual variability, can optionally be added to library
ltbs: log-transform both sides. Not used in simulations, only for fitting (sets attribute ltbs).
misc: a list of miscellaneous model metadata
cmt_mapping: list indicating which administration routes apply to which compartments. Example: list("oral" = 1, "infusion" = 2)
int_step_size: step size for integrator. Can be pre-specified for model, to override default for sim_ode()
default_parameters: population or specific patient values, can optionally be added to library
fixed: parameters that should not have iiv added.
cpp_show_code: show generated C++ code
package: package name when saving as package
test_file: optional test file to be included with package
install: install package after compilation?
folder: base folder name to create package in
lib_location: install into folder (--library argument)
verbose: show more output
as_is: use C-code as-is, don't substitute line-endings or shift indices
nonmem: add NONMEM code as attribute to model object
comments: comments for model
version: number of library
quiet: passed on to system2 as setting for stderr and stdout; how to output cmd line output. Default ("") is R console, NULL or FALSE discards. TRUE captures the output and saves as a file.
definition: optional, filename for the JSON file the full definition for the model. The definition file will be stored as definition.json in the resulting package.